Essential Divalent Metal Research Articles

Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-.ANG. resolution: identification of the active site and possible catalytic residues

The crystal structure of mandelate racemase (MR) has been solved at 3.0-A resolution by multiple isomorphous replacement and subsequently refined against X-ray diffraction data to 2.5-A resolution by use of both molecular dynamics refinement (XPLOR) and restrained least-squares refinement (PROLSQ). The current crystallographic R-factor for this structure is 18.3%. MR is composed of two major structural domains and a third, smaller, C-terminal domain. The N-terminal domain has an alpha + beta topology consisting of a three-stranded antiparallel beta-sheet followed by an antiparallel four alpha-helix bundle. The central domain is a singly wound parallel alpha/beta-barrel composed of eight central strands of beta-sheet and seven alpha-helices. The C-terminal domain consists of an irregular L-shaped loop with several short sections of antiparallel beta-sheet and two short alpha-helices. This C-terminal domain partially covers the junction between the major domains and occupies a region of the central domain that is filled by an eight alpha-helix in all other known parallel alpha/beta-barrels except for the barrel domain in muconate lactonizing enzyme (MLE) [Goldman, A., Ollis, D. L., & Steitz, T. A. (1987) J. Mol. Biol. 194, 143] whose overall polypeptide fold and amino acid sequence are strikingly similar to those of MR [Neidhart, D. J., Kenyon, G. L., Gerlt, J. A., & Petsko, G. A. (1990) Nature 347, 692]. In addition, the crystal structure reveals that, like MLE, MR is tightly packed as an octamer of identical subunits. The active site of MR is located between the two major domains, at the C-terminal ends of the beta-strands in the alpha/beta-barrel domain. The catalytically essential divalent metal ion is ligated by three side-chain carboxyl groups contributed by residues of the central beta-sheet. A model of a productive substrate complex of MR has been constructed on the basis of difference Fourier analysis at 3.5-A resolution of a complex between MR and (R,S)-p-iodomandelate, permitting identification of residues that may participate in substrate binding and catalysis. The ionizable groups of both Lys 166 and His 297 are positioned to interact with the chiral center of substrate, suggesting that both of these residues may function as acid/base catalysts.(ABSTRACT TRUNCATED AT 400 WORDS)

Metal binding to DNA polymerase I, its large fragment, and two 3‘,5‘-exonuclease mutants of the large fragment.

DNA polymerase I (Pol I) is an enzyme of DNA replication and repair containing three active sites, each requiring divalent metal ions such as Mg2+ or Mn2+ for activity. As determined by EPR and by 1/T1 measurements of water protons, whole Pol I binds Mn2+ at one tight site (KD = 2.5 microM) and approximately 20 weak sites (KD = 600 microM). All bound metal ions retain one or more water ligands as reflected in enhanced paramagnetic effects of Mn2+ on 1/T1 of water protons. The cloned large fragment of Pol I, which lacks the 5',3'-exonuclease domain, retains the tight metal binding site with little or no change in its affinity for Mn2+, but has lost approximately 12 weak sites (n = 8, KD = 1000 microM). The presence of stoichiometric TMP creates a second tight Mn2+ binding site or tightens a weak site 100-fold. dGTP together with TMP creates a third tight Mn2+ binding site or tightens a weak site 166-fold. The D424A (the Asp424 to Ala) 3',5'-exonuclease deficient mutant of the large fragment retains a weakened tight site (KD = 68 microM) and has lost one weak site (n = 7, KD = 3500 microM) in comparison with the wild-type large fragment, and no effect of TMP on metal binding is detected. The D355A, E357A (the Asp355 to Ala, Glu357 to Ala double mutant of the large fragment of Pol I) 3',5'-exonuclease-deficient double mutant has lost the tight metal binding site and four weak metal binding sites. The binding of dGTP to the polymerase active site of the D355A,E357A double mutant creates one tight Mn2+ binding site with a dissociation constant (KD = 3.6 microM), comparable with that found on the wild-type enzyme, which retains one fast exchanging water ligand. Mg2+ competes at this site with a KD of 100 microM. It is concluded that the single tightly bound Mn2+ on Pol I and a weakly bound Mn2+ which is tightened 100-fold by TMP are at the 3',5'-exonuclease active site and are essential for 3',5'-exonuclease activity, but not for polymerase activity. Additional weak Mn2+ binding sites are detected on the 3',5'-exonuclease domain, which may be activating, and on the polymerase domain, which may be inhibitory. The essential divalent metal activator of the polymerase reaction requires the presence of the dNTP substrate for tight metal binding indicating that the bound substrate coordinates the metal.(ABSTRACT TRUNCATED AT 400 WORDS)

Effects of essential divalent metals on carcinogenicity and metabolism of nickel and cadmium

Interactions between the physiologically essential metals calcium, magnesium, and zinc and the carcinogenic metals nickel and cadmium were investigated to help elucidate the mechanisms of action of the carcinogenic metals. Bioassay studies revealed several significant findings, including: (1) the ability of magnesium and calcium to inhibit nickel-induced elevation of pulmonary adenoma incidence in strain A mice; (2) the ability of magnesium, but not of calcium, to prevent cadmium-induced subcutaneous sarcoma formation; and (3) the ability of magnesium, but not of calcium, to inhibit nickel-induced muscle tumor formation. Biochemical studies indicated a direct relationship between the antitumorigenic potential of magnesium and the capacity of this metal to: (1) inhibit nickel and cadmium uptake by the target tissues in vivo; (2) inhibit nickel-induced disturbances in DNA synthesis in vivo; (3) inhibit nuclear and cytosolic uptake of nickel by the target tissue cells in vivo; and (4) inhibit nickel and cadmium binding to DNA in vitro. Calcium, which in most cases did not prevent carcinogenesis, had no consistent influence on the uptake of carcinogenic metals or their biochemical effects in the target tissues. Magnesium and zinc, but not calcium, were also found to attenuate the acute toxic effects of nickel, indicating a possible correlation between prevention of acute effects and reduction in tumorigenicity. Zinc, which antagonizes cadmium tumorigenicity in the rat testis, was found to reduce markedly cadmium uptake into isolated testicular interstitial cells. Also, zinc was found to inhibit strongly cadmium binding to DNA in vitro.

Antagonism by essential divalent metals and amino acids of nickel(II)-DNA binding in vitro

In vitro binding of nickel(II) to DNA and the effects of divalent essential metals calcium, magnesium, manganese, copper, and zinc, and of amino acids histidine, cysteine, glutamine, arginine, lysine, alanine, and glycine upon that binding were investigated. Samples of 0.156 mg of calf thymus DNA (0.078 mg/ml in 5 m m ammonium acetate buffer, pH = 7.4) were incubated for 1 hr at 24°C with various concentrations of nickel(II)acetate labeled with 63Ni (0.1 to 250 μ m) in the absence or presence of 50 μ m concentrations of the essential metal acetates, or with 100 μ m concentrations of the amino acids. Free and DNA-bound nickel(II) fractions were separated by gel filtration on Sephadex G-25 and quantified by liquid scintillation counting. Scatchard analysis revealed more than two types of nickel(II)-binding sites and a positive cooperativity of binding at the bound-Ni concentrations below 0.35 μ m. The high-affinity nickel(II)-binding sites at DNA were identified as phosphate groups. Their binding capacity equalled 0.043 μmol/mg DNA (approx, 1 mol Ni 70 mol of DNA bases). The apparent dissociation constant of nickel(II) from the high-affinity sites was 5.35 μ m. Double reciprocal plots showed the essential divalent metals to be competitive antagonists of nickel(II)-binding to the high-affinity sites, ranking Mg(II) ≥ Mn(II) > Ca(II) ≥ Cu(II) = Zn(II). Similarly, the amino acids antagonized nickel binding to DNA with a relative strength of His > Gln ≥ His Cys > Arg > Cys ≥ Gly = Ala ≥ Lys . The strongest inhibitors of nickel(II)-DNA binding in vitro appear to be magnesium and manganese, i.e., the same metals that are capable of attenuating nickel carcinogenicity in vivo.

Differences in the responses of brain cytosolic and mitochondrial hexokinases to three essential divalent metal ions

1. Rat brain cytosolic and mitochondrial hexokinase activities were undetectable without added divalent cations. 2. Mg 2+ activated cytosolic ( K 0.5 of Mg 2+ = 343 ± 13 μM) and mitochondrial ( K 0.5 of Mg 2+ = 183 ± 8 μM) hexokinase in a concentration-related manner. The corresponding values for Mn 2+ were 702 ± 99 and 413 ± 21 μM respectively. 3. Ca 2+, however, activated both forms of hexokinase poorly. 4. In the presence of Mg 2+, both Mn 2+ and Cu 2+ were more potent inhibitors of cytosolic hexokinase than mitochondrial hexokinase, whereas the inhibition of Cd 2+ and Ca 2+ did not show such selectivity. 5. These results demonstrate that brain mitochondrial and cytosolic hexokinases differ significantly in their responses to divalent cations.